Next-generation sequencing technologies for detection of modified nucleotides in RNAs

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

(2016) Konstantin Licht et al.   JOURNAL OF CELL BIOLOGY

Analysis of RNA modifications by liquid chromatography–tandem mass spectrometry

(2016) Kathrin Thüring et al.   METHODS

N 6-Methyladenosine (m6A) Methylation in mRNA with A Dynamic and Reversible Epigenetic Modification

(2016) Ruifan Wu et al.   MOLECULAR BIOTECHNOLOGY

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

(2016) Benoit Molinie et al.   NATURE METHODS

Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA

(2016) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

An updated human snoRNAome

(2016) Hadi Jorjani et al.   NUCLEIC ACIDS RESEARCH

Going global: the new era of mapping modifications in RNA

(2016) Patrick A. Limbach et al.   Wiley Interdisciplinary Reviews-RNA

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method

(2015) Tsutomu Suzuki et al.   Nature Protocols

The reverse transcription signature ofN-1-methyladenosine in RNA-Seq is sequence dependent

(2015) Ralf Hauenschild et al.   NUCLEIC ACIDS RESEARCH

NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs

(2015) Sara Haag et al.   RNA

Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120

(2015) Gabrielle Bourgeois et al.   PLoS One

Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

(2014) Ulf Birkedal et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

(2014) M. Sakurai et al.   GENOME RESEARCH

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs

(2014) Hana Cahová et al.   NATURE

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP

(2014) Vahid Khoddami et al.   Nature Protocols

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

(2014) Stefanie Kellner et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability

(2014) Andriana Gigova et al.   RNA

LC–MS of oligonucleotides: applications in biomedical research

(2014) Babak Basiri et al.   Bioanalysis

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

(2013) N. Liu et al.   RNA

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription

(2013) Igor D Vilfan et al.   JOURNAL OF NANOBIOTECHNOLOGY

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

(2012) Francesca Tuorto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

Reversible RNA adenosine methylation in biological regulation

(2012) Guifang Jia et al.   TRENDS IN GENETICS

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Cellular Dynamics of RNA Modification

(2011) Chengqi Yi et al.   ACCOUNTS OF CHEMICAL RESEARCH

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Applications of mass spectrometry to the study of siRNA

(2010) Michael B. Beverly   MASS SPECTROMETRY REVIEWS

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH